A novel class of microRNA-recognition elements that function only within open reading frames

Small Nucleolar RNA Host Gene 1 (SNHG1) and Chromosome 2 Open Reading Frame 48 (C2orf48) as Potential Prognostic Signatures for Liver Cancer by Constructing Regulatory Networks

Background

Liver cancer is a common malignant tumor with poor prognosis. The present study sought to identify potential signatures that can predict the prognosis of patients with liver cancer.

Material/Methods

The RNA sequencing (RNA-seq) and clinical information of liver cancer patients were obtained from the Cancer Genome Atlas (TCGA) database. Differentially expressed long noncoding RNAs (lncRNAs), microRNAs (miRNAs), and messenger RNAs (mRNAs) were identified between liver cancer and adjacent normal tissues. After predicting lncRNA–miRNA and miRNA–mRNA pairs using online databases, the competing endogenous RNA (ceRNA) networks were constructed. Furthermore, the prognostic value of these differentially expressed genes was evaluated using univariate and multivariate Cox regression analyses.

Results

After constructing the ceRNA network, 2 lncRNAs small nucleolar RNA host gene 1 (SNHG1) and chromosome 2 open reading frame 48 (C2orf48) with the most nodes were identified. Correlation analysis revealed that SNHG1 was correlated with miR-195 and C2orf48 was correlated with miR-195 and miR-93. High expression of SNHG1, C2orf48, and miR-93 can contribute to poorer clinical outcomes compared to low expression. Furthermore, low miR-195 expression was correlated with shorter survival time than was high expression. SNHG1 and C2orf48 were closely associated with histology grade. Univariate and multivariate Cox regression analyses confirmed that SNHG1 and C2orf48 are risk factors for liver cancer.

Conclusions

Our findings revealed that SNHG1 and C2orf48 possess potential prognostic value and should be considered as possible biomarkers for predicting clinical outcomes for patients with liver cancer.

The Role of Dynamic miRISC During Neuronal Development

Activity-dependent protein synthesis plays an important role during neuronal development by fine-tuning the formation and function of neuronal circuits. Recent studies have shown that miRNAs are integral to this regulation because of their ability to control protein synthesis in a rapid, specific and potentially reversible manner. miRNA mediated regulation is a multistep process that involves inhibition of translation before degradation of targeted mRNA, which provides the possibility to store and reverse the inhibition at multiple stages. This flexibility is primarily thought to be derived from the composition of miRNA induced silencing complex (miRISC). AGO2 is likely the only obligatory component of miRISC, while multiple RBPs are shown to be associated with this core miRISC to form diverse miRISC complexes. The formation of these heterogeneous miRISC complexes is intricately regulated by various extracellular signals and cell-specific contexts. In this review, we discuss the composition of miRISC and its functions during neuronal development. Neurodevelopment is guided by both internal programs and external cues. Neuronal activity and external signals play an important role in the formation and refining of the neuronal network. miRISC composition and diversity have a critical role at distinct stages of neurodevelopment. Even though there is a good amount of literature available on the role of miRNAs mediated regulation of neuronal development, surprisingly the role of miRISC composition and its functional dynamics in neuronal development is not much discussed. In this article, we review the available literature on the heterogeneity of the neuronal miRISC composition and how this may influence translation regulation in the context of neuronal development.

An ortholog of the Vasa intronic gene is required for small RNA-mediated translation repression in Chlamydomonas reinhardtii

Small RNAs (sRNAs) are a class of noncoding RNAs that regulate complementary mRNAs, by triggering translation repression and/or transcript decay, and influence multiple biological processes. In animals, land plants, and some protists like the alga Chlamydomonas, sRNAs can repress translation of polyribosome-associated mRNAs, without or with only minimal transcript destabilization. However, the precise silencing mechanism is poorly understood. We found that Chlamydomonas VIG1, a homolog of the Drosophila melanogaster Vasa intronic gene and a member of a widely conserved protein family in eukaryotes, is involved in this process. VIG1 appears to be an ancillary ribosomal constituent. Additionally, VIG1 copurifies with core components of sRNA effector complexes and plays a key role in the sRNA-mediated translation repression of polyribosomal transcripts.

Small RNAs (sRNAs) associate with Argonaute (AGO) proteins in effector complexes, termed RNA-induced silencing complexes (RISCs), which regulate complementary transcripts by translation inhibition and/or RNA degradation. In the unicellular alga Chlamydomonas, several metazoans, and land plants, emerging evidence indicates that polyribosome-associated transcripts can be translationally repressed by RISCs without substantial messenger RNA (mRNA) destabilization. However, the mechanism of translation inhibition in a polyribosomal context is not understood. Here we show that Chlamydomonas VIG1, an ortholog of the Drosophila melanogaster Vasa intronic gene (VIG), is required for this process. VIG1 localizes predominantly in the cytosol and comigrates with monoribosomes and polyribosomes by sucrose density gradient sedimentation. A VIG1-deleted mutant shows hypersensitivity to the translation elongation inhibitor cycloheximide, suggesting that VIG1 may have a nonessential role in ribosome function/structure. Additionally, FLAG-tagged VIG1 copurifies with AGO3 and Dicer-like 3 (DCL3), consistent with it also being a component of the RISC. Indeed, VIG1 is necessary for the repression of sRNA-targeted transcripts at the translational level but is dispensable for cleavage-mediated RNA interference and for the association of the AGO3 effector with polyribosomes or target transcripts. Our results suggest that VIG1 is an ancillary ribosomal component and plays a role in sRNA-mediated translation repression of polyribosomal transcripts.

The biochemical basis of microRNA targeting efficacy

MicroRNAs (miRNAs) act within Argonaute proteins to guide repression of messenger RNA targets. Although various approaches have provided insight into target recognition, the sparsity of miRNA-target affinity measurements has limited understanding and prediction of targeting efficacy. Here, we adapted RNA bind-n-seq to enable measurement of relative binding affinities between Argonaute-miRNA complexes and all sequences ≤12 nucleotides in length. This approach revealed noncanonical target sites specific to each miRNA, miRNA-specific differences in canonical target-site affinities, and a 100-fold impact of dinucleotides flanking each site. These data enabled construction of a biochemical model of miRNA-mediated repression, which was extended to all miRNA sequences using a convolutional neural network. This model substantially improved prediction of cellular repression, thereby providing a biochemical basis for quantitatively integrating miRNAs into gene-regulatory networks.

The MicroRNA Centrism in the Orchestration of Neuroinflammation in Neurodegenerative Diseases

MicroRNAs (miRNAs) are small non-coding RNAs with a unique ability to regulate the transcriptomic profile by binding to complementary regulatory RNA sequences. The ability of miRNAs to enhance (proinflammatory miRNAs) or restrict (anti-inflammatory miRNAs) inflammatory signalling within the central nervous system is an area of ongoing research, particularly in the context of disorders that feature neuroinflammation, including neurodegenerative diseases (NDDs). Furthermore, the discovery of competing endogenous RNAs (ceRNAs) has led to an increase in the complexity of miRNA-mediated gene regulation, with a paradigm shift from a unidirectional to a bidirectional regulation, where miRNA acts as both a regulator and is regulated by ceRNAs. Increasing evidence has revealed that ceRNAs, including long non-coding RNAs, circular RNAs, and pseudogenes, can act as miRNA sponges to regulate neuroinflammation in NDDs within complex cross-talk regulatory machinery, which is referred to as ceRNA network (ceRNET). In this review, we discuss the role of miRNAs in neuroinflammatory regulation and the manner in which cellular and vesicular ceRNETs could influence neuroinflammatory dynamics in complex multifactorial diseases, such as NDDs.

Nonconserved miR-608 suppresses prostate cancer progression through RAC2/PAK4/LIMK1 and BCL2L1/caspase-3 pathways by targeting the 3'-UTRs of RAC2/BCL2L1 and the coding region of PAK4

The aim of this study is to investigate the functions and mechanisms of miR-608 in prostate cancer (PCa). CISH and qRT-PCR analysis demonstrated that miR-608 was low expressed in PCa tissues and cells, which was partly attributed to the methylation of CpG island adjacent to the transcription start site (TSS) of miR-608 gene. Intracellular miR-608 overexpression inhibited in vivo PCa tumor growth, and suppressed PCa cell proliferation, G2/M transition, and migration in vitro, which was independent of EMT-associated mechanisms. Then RAC2, a GTPase previously deemed hematopoiesis-specific but now discovered to exist and play important roles in PCa, was verified by western blot and dual-luciferase reporter assays to mediate the effects of miR-608 through RAC2/PAK4/LIMK1/cofilin pathway. MiR-608 also promoted the apoptosis of PCa cells through BCL2L1/caspase-3 pathway by targeting the 3'-UTR of BCL2L1. Moreover, PAK4, the downstream effector of RAC2, was found to be targeted by miR-608 at the mRNA coding sequence (CDS) instead of the canonical 3'-UTR. Knocking down RAC2, PAK4, or BCL2L1 with siRNAs reproduced the antiproliferative, mitosis-obstructive, antimigratory and proapoptotic effects of miR-608 in PCa cells, which could be attenuated by downregulating miR-608. In conclusion, miR-608 suppresses PCa progression, and its activation provides a new therapeutic option for PCa.

Identification of murine gammaherpesvirus 68 miRNA-mRNA hybrids reveals miRNA target conservation among gammaherpesviruses including host translation and protein modification machinery

Gammaherpesviruses, including the human pathogens Epstein-Barr virus (EBV) and Kaposi’s sarcoma-associated herpesvirus (KSHV), establish lifelong latent infection in B cells and are associated with a variety of tumors. In addition to protein coding genes, these viruses encode numerous microRNAs (miRNAs) within their genomes. While putative host targets of EBV and KSHV miRNAs have been previously identified, the specific functions of these miRNAs during in vivo infection are largely unknown. Murine gammaherpesvirus 68 (MHV68) is a natural pathogen of rodents that is genetically related to both EBV and KSHV, and thus serves as an excellent model for the study of EBV and KSHV genetic elements such as miRNAs in the context of infection and disease. However, the specific targets of MHV68 miRNAs remain completely unknown. Using a technique known as qCLASH (quick crosslinking, ligation, and sequencing of hybrids), we have now identified thousands of Ago-associated, direct miRNA-mRNA interactions during lytic infection, latent infection and reactivation from latency. Validating this approach, detailed molecular analyses of specific interactions demonstrated repression of numerous host mRNA targets of MHV68 miRNAs, including Arid1a, Ctsl, Ifitm3 and Phc3. Notably, of the 1,505 MHV68 miRNA-host mRNA targets identified in B cells, 86% were shared with either EBV or KSHV, and 64% were shared among all three viruses, demonstrating significant conservation of gammaherpesvirus miRNA targeting. Pathway analysis of MHV68 miRNA targets further revealed enrichment of cellular pathways involved in protein synthesis and protein modification, including eIF2 Signaling, mTOR signaling and protein ubiquitination, pathways also enriched for targets of EBV and KSHV miRNAs. These findings provide substantial new information about specific targets of MHV68 miRNAs and shed important light on likely conserved functions of gammaherpesvirus miRNAs.

Gammaherpesviruses, including the human pathogens Epstein-Barr virus (EBV) and Kaposi’s sarcoma-associated herpesvirus (KSHV), establish lifelong infections and are associated with a variety of tumors. These viruses encode numerous molecules called microRNAs (miRNAs) within their genomes, which target and suppress the products of specific genes within infected host cells. However, the function of these miRNAs during in vivo infection is largely unknown. Murine gammaherpesvirus 68 (MHV68) is a natural pathogen of rodents that is genetically related to both EBV and KSHV, and thus serves as an excellent model for the study of EBV and KSHV. Here, we describe the identification and validation of thousands of new MHV68 miRNA targets. Notably, 86% of the MHV68 miRNA targets identified were shared with either EBV or KSHV, and 64% were shared among all three viruses. Further analyses revealed enrichment of cellular pathways involved in protein synthesis and protein modification, including pathways also enriched for targets of EBV and KSHV miRNAs. These findings provide substantial new information about specific targets of MHV68 miRNAs and shed important light on likely conserved functions of gammaherpesvirus miRNAs.

Ribosome clearance during RNA interference

In the course of identifying and cleaving RNA, the RNAi machinery must encounter and contend with the megadalton-sized ribosomes that carry out translation. We investigated this interface by examining the fate of actively translated mRNAs subjected to RNAi in C. elegans Quantifying RNA levels (RNA-seq) and ongoing translation (Ribo-seq), we found there is a greater fold repression of ongoing translation than expected from loss of RNA alone, observing stronger translation repression relative to RNA repression for multiple, independent double-stranded RNA triggers, and for multiple genes. In animals that lack the RNA helicase SKI complex and the ribosome rescue factor PELOTA, ribosomes stall on the 3' edges of mRNAs at and upstream of the RNAi trigger. One model to explain these observations is that ribosomes are actively cleared from mRNAs by SKI and PELO during or following mRNA cleavage. Our results expand prior studies that show a role for the SKI RNA helicase complex in removing RNA targets following RNAi in flies and plants, illuminating the widespread role of the nonstop translation surveillance in RNA silencing during RNAi. Our results are also consistent with proposals that RNAi can attack messages during active translation.

RNA structural analysis of the MYC mRNA reveals conserved motifs that affect gene expression

The MYC gene encodes a human transcription factor and proto-oncogene that is dysregulated in over half of all known cancers. To better understand potential post-transcriptional regulatory features affecting MYC expression, we analyzed secondary structures in the MYC mRNA using a program that is optimized for finding small locally-folded motifs with a high propensity for function. This was accomplished by calculating folding metrics across the MYC sequence using a sliding analysis window and generating unique consensus base pairing models weighted by their lower-than-random predicted folding energy. A series of 30 motifs were identified, primarily in the 5' and 3' untranslated regions, which show evidence of structural conservation and compensating mutations across vertebrate MYC homologs. This analysis was able to recapitulate known elements found within an internal ribosomal entry site, as well as discover a novel element in the 3' UTR that is unusually stable and conserved. This novel motif was shown to affect MYC expression, potentially via the modulation of miRNA target accessibility or other trans-regulatory factors. In addition to providing basic insights into mechanisms that regulate MYC expression, this study provides numerous, potentially druggable RNA targets for the MYC gene, which is considered “undruggable” at the protein level.

Identification of a miRNA-mRNA network associated with lymph node metastasis in colorectal cancer

Lymph node metastasis is an important step in the progression of colorectal cancer (CRC); however, the underlying mechanisms are still unknown. The aim of the present study was to identify the gene expression pattern during lymph node metastasis in CRC and to identify upstream microRNAs (miRNAs) to explore the underlying mechanisms in detail. A total of 305 differently expressed genes (DEGs) were identified, including 227 upregulated genes and 78 downregulated genes in lymph node metastasis. Pathway and process enrichment analysis demonstrated that DEGs were significantly enriched in ‘NABA CORE MATRISOME’, ‘extracellular matrix assembly’, ‘antimicrobial humoral response’ and ‘Toll-like receptor signaling’ pathways. The top 10 hub genes were identified by protein-protein interaction network, and sub-networks revealed that these genes were involved in significant pathways, including ‘neutrophil chemotaxis’ and ‘Smooth Muscle Contraction’. In addition, 73 mature differently expressed miRNAs associated with lymph node metastasis were identified, of which 48 were upregulated and 25 were downregulated. Six miRNAs were identified to regulate DEGs. Additionally, based on the relationship between miRNAs and transcription factors, a miRNA-TF-mRNA network was constructed. In conclusion, DEGs, miRNAs and their interactions and pathways were identified in lymph node metastasis in CRC, which provided insight into the mechanism of CRC metastasis and may be used to develop novel targets for CRC treatment.

Non-coding RNA regulation in reproduction: Their potential use as biomarkers

Non-coding RNAs (ncRNAs) are crucial regulatory elements in most biological processes and reproduction is also controlled by them. The different types of ncRNAs, as well as the high complexity of these regulatory pathways, present a complex scenario; however, recent studies have shed some light on these questions, discovering the regulatory function of specific ncRNAs on concrete reproductive biology processes. This mini review will focus on the role of ncRNAs in spermatogenesis and oogenesis, and their potential use as biomarkers for reproductive diseases or for reproduction success.

miRNA length variation during macrophage stimulation confounds the interpretation of results: implications for miRNA quantification by RT-qPCR

Most microRNAs (miRNAs) are expressed as a mix of length isoforms (referred to as isomiRs). IsomiR stoichiometry can be differentially impacted upon cell stimulation, as recently evidenced by our group in the context of immune responses induced by type-I interferon (IFN). Here, we revisit published RNA-seq data sets of human and mouse macrophages stimulated with bacterial products at the isomiR level. We demonstrate that for several miRNAs, macrophage stimulation induces changes in isomiR stoichiometry. Critically, we find that changes in miRNA expression can be misinterpreted when miRNAs are quantified by RT-qPCR, as primers directed against canonical miRNA sequences may not equally target the different isomiRs that are regulated endogenously. Beyond the case of phagocyte stimulation, our analyses reinforce the concept that analysis of miRNA expression at the isoform level should become standard practice.

miRNA Targeting: Growing beyond the Seed

miRNAs are small RNAs that guide Argonaute proteins to specific target mRNAs to repress their translation and stability. Canonically, miRNA targeting is reliant on base pairing of the seed region, nucleotides 2-7, of the miRNA to sites in mRNA 3' untranslated regions. Recently, the 3' half of the miRNA has gained attention for newly appreciated roles in regulating target specificity and regulation. In addition, the extent of pairing to the miRNA 3' end can influence the stability of the miRNA itself. These findings highlight the importance of sequences beyond the seed in controlling the function and existence of miRNAs.

Contemporary Ribonomics Methods for Viral microRNA Target Analysis

Numerous cellular processes are regulated by microRNAs (miRNAs), both cellular and viral. Elucidating the targets of miRNAs has become an active area of research. An important method in this field is cross-linking and immunoprecipitation (CLIP), where cultured cells or tissues are UV-irradiated to cross-link protein and nucleic acid, the RNA binding protein of interest is immunoprecipitated, and the RNAs pulled down with the protein are isolated, reverse-transcribed, and analyzed by sequencing. CLIP using antibody against Argonaute (Ago), which binds to both miRNA and mRNA as they interact in RISC, has allowed researchers to uncover a large number of miRNA targets. Coupled with high-throughput sequencing, CLIP has been useful for revealing miRNA targetomes for the γ-herpesviruses Kaposi's sarcoma-associated herpesvirus (KSHV) and Epstein-Barr virus (EBV). Variants on the CLIP protocol are described, with the benefits and drawbacks of each. In particular, the most recent methods involving RNA⁻RNA ligation to join the miRNA and its RNA target have aided in target identification. Lastly, data supporting biologically meaningful interactions between miRNAs and long non-coding RNAs (lncRNAs) are reviewed. In summary, ribonomics-based miRNA targetome analysis has expanded our understanding of miRNA targeting and has provided a rich resource for EBV and KSHV research with respect to pathogenesis and tumorigenesis.